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/dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/t/rings/
H A Dmirror.ring4 Ring: atoms(a1 a2 a3); bonds(b1 b2 b3); aromatic(0)
5 Ring: atoms(a1 a3 a2); bonds(b3 b2 b1); aromatic(0)
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Ring-0.19/t/rings/
H A Dmirror.ring4 Ring: atoms(a1 a2 a3); bonds(b1 b2 b3); aromatic(0)
5 Ring: atoms(a1 a3 a2); bonds(b3 b2 b1); aromatic(0)
/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/
H A Dwrite.pl15 unique => $unique, aromatic => $aromatic);
H A DSMILES.pm479 $opts{aromatic} = 1; # all unique smiles have to be aromatic
485 if ($opts{aromatic}) {
610 return '' if $opts->{aromatic} && $bond->aromatic;
618 $symbol = lc $symbol if $opts->{aromatic} && $atom->aromatic;
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/
H A Dwrite.pl15 unique => $unique, aromatic => $aromatic);
/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/
H A Dbond.h101 bool aromatic() { in aromatic() function
104 if (start->aromatic && end->aromatic) in aromatic()
/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/M_Kossner/
H A DBaseFeatures_DIP2_NoMicrospecies.fdef20 # aromatic N, but not indole or pyrole or fusing two rings or tetrazole
23 # tertiary nitrogen adjacent to aromatic carbon
29 # Removed aromatic sulfur from ChalcAcceptor definition
30 #We will not use aromatic oxygens! cf Leach, Gillet ... J Med Chem 2010,53, 539-558
91 # guanidine group is positively charged (too promiscuous? We do not match any aromatic systems here…
103 # aromatic rings of various sizes:
109 # match things like 'o1c2cccc2ccc1', which have an aromatic unit spread across multiple simple
150 # 6.2009 (MK): aromatic c is not per se a hydrophobic atom
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Ring-0.19/t/rings2/
H A Dnorbornane.ring3 Ring: atoms(a1 a2 a3 a4 a5); bonds(b1 b2 b3 b4 b5); aromatic(0)
4 Ring: atoms(a1 a2 a3 a6 a7); bonds(b1 b2 b6 b7 b8); aromatic(0)
H A Dbiphenyl.ring3 Ring: atoms(a1 a6 a5 a4 a3 a2); bonds(b6 b5 b4 b3 b2 b1); aromatic(1)
4 Ring: atoms(a7 a12 a11 a10 a9 a8); bonds(b13 b12 b11 b10 b9 b8); aromatic(1)
/dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/t/rings2/
H A Dnorbornane.ring3 Ring: atoms(a1 a2 a3 a4 a5); bonds(b1 b2 b3 b4 b5); aromatic(0)
4 Ring: atoms(a1 a2 a3 a6 a7); bonds(b1 b2 b6 b7 b8); aromatic(0)
H A Dbiphenyl.ring3 Ring: atoms(a1 a6 a5 a4 a3 a2); bonds(b6 b5 b4 b3 b2 b1); aromatic(1)
4 Ring: atoms(a7 a12 a11 a10 a9 a8); bonds(b13 b12 b11 b10 b9 b8); aromatic(1)
/dports/science/gromacs/gromacs-2021.4/docs/reference-manual/special/
H A Dremove-fast-dgf.rst44 planarity mostly deal with aromatic residues. Bonds, angles, and
52 are virtualized, those inside the aromatic residues will be virtualized
53 as well, *i.e.* hydrogens in the aromatic residues are treated
54 differently depending on the treatment of the aromatic residues. Note
55 further that the virtualization of aromatic rings is deprecated.
60 constructions for the aromatic residues are based on the bond lengths
63 construction needed for a whole aromatic group.
115 - *single amine or amide (-NH-) and aromatic hydrogens
161 Out-of-plane vibrations in aromatic groups
164 The planar arrangements in the side chains of the aromatic residues
[all …]
/dports/science/p5-Chemistry-Pattern/Chemistry-Pattern-0.27/Pattern/
H A DBond.pm51 return ($what->order eq $where->order) || ($where->aromatic && $what->aromatic);
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/t/
H A Dnames.t14 my $out = $mol->print(format => 'smiles', aromatic => 1) . "\t" . $mol->name;
16 $out = $mol->print(format => 'smiles', name => 1, aromatic => 1);
/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/t/
H A Dnames.t14 my $out = $mol->print(format => 'smiles', aromatic => 1) . "\t" . $mol->name;
16 $out = $mol->print(format => 'smiles', name => 1, aromatic => 1);
/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/others/isdb-1/charmm36-eef1sb.ff/
H A Datomtypes.atp11 CA 12.01100 ; aromatic C
13 CAI 12.01100 ; aromatic C next to CPT in trp
85 CG2R61 12.01100 ; 6-mem aromatic C
87 CG2R63 12.01100 ; 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?)
89 CG2R66 12.01100 ; 6-mem aromatic carbon bound to F
90 CG2R67 12.01100 ; 6-mem aromatic carbon of biphenyl
125 CN3 12.01100 ; Nucleic acid aromatic carbon
126 CN3T 12.01100 ; Nucleic acid aromatic carbon, Thy C5
163 FGR1 18.99800 ; aromatic fluorine
215 HGR61 1.00800 ; aromatic H
[all …]
/dports/biology/babel/babel-1.6/
H A Dtosmiles.c227 int aromatic; /* TRUE if ANY of the bonds to it are aromatic */ member
265 initatomdata.aromatic = FALSE; in generatesmilesstring()
288 atomdata[natoms].aromatic = hasaromaticbonds(&frag->atom[atom]); in generatesmilesstring()
426 smileslen += addsmilesatom(tmpstr, atomdata[a].symbol, atomdata[a].aromatic); in generatesmilesstring()
462 smipos += addsmilesatom(&smiles[smipos], atomdata[a].symbol, atomdata[a].aromatic); in generatesmilesstring()
501 addsmilesatom(char *string, char *symbol, int aromatic) in addsmilesatom() argument
517 string[n++] = (aromatic) ? tolower(symbol[0]) : symbol[0]; in addsmilesatom()
521 string[n++] = (aromatic) ? tolower(symbol[1]) : symbol[1]; in addsmilesatom()
/dports/science/openbabel/openbabel-3.1.1/data/
H A Dgenheaders.sh3 ./bin2hex.pl aromatic.txt AromaticData >aromatic.h
/dports/science/gromacs/gromacs-2021.4/share/top/amber03.ff/
H A Datomtypes.atp4 CA 12.01000 ; sp2 C pure aromatic (benzene)
5 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
6 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
9 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amber99.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amber94.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amber96.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amber99sb.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amber99sb-ildn.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
/dports/science/gromacs/gromacs-2021.4/share/top/amberGS.ff/
H A Datomtypes.atp3 CA 12.01000 ; sp2 C pure aromatic (benzene)
4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)

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